Hi,
The error comes from the fact that you have not specified an output
filename.
It will not fill one in automatically - you have to specify it.
The length of filename is fine.
Just use the structural_brain as input, like you are doing now, and
specify
an output name and all should be well.
All the best,
Mark
On 13 Feb 2008, at 19:08, Emily Stoneham wrote:
> Hello again. I am new to fMRI and to FSL, so forgive me if this is
> an ignorant question, but in
> FLIRT, (using the feeds data to learn the system) it defaults to a
> reference image of:
> /Users/MLE/fsl/data/standard/MNI152_T1_2mm_brain
>
> What do I put in for an input image? I assume that I want a
> structural, so I was using
> /Users/MLE/Desktop/FSL/feeds/data/structural_brain.nii.gz
>
> and I assume as well that it should default to some output image?
> I.e., I don't put that in myself?
>
> When I hit 'go', it gives me this error:
>
> /Users/MLE/fsl/bin/flirt -in /Users/MLE/Desktop/FSL/feeds/data/
> structural_brain.nii.gz -ref
> /Users/MLE/fsl/data/standard/MNI152_T1_2mm_brain -out -omat .mat -
> bins 256 -cost corratio
> -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp
> trilinear
> WARNING: change in option usage
>
> To specify the input volume the option -in should be used
> Accepting the filename for now, but please update to new syntax in
> future.
>
> ** ERROR (nifti_image_read): failed to find header file for '.mat'
> ** ERROR: nifti_image_open(.mat): bad header info
> Error: failed to open file .mat
> ERROR: Could not open image .mat
> Image Exception : #22 :: Failed to read volume .mat
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> Finished
>
>
> A) am I using the wrong images? If so, what images am I to use?
> B) What does this error mean?
> C) could it be that it doesn't like the length of the filename?
> That it has to go too deep for the
> data (through too many folders)?
>
> Thanks!
> Emily
>
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